OpenRaiser/Intern-Atlas huggingface dataset:
BIOME-Bench: A Benchmark for Biomolecular Interaction Inference and Multi-Omics Pathway Mechanism Elucidation from Scientific Literature
Venue: arXiv cs.CL 2025
Year: 2025

Multi-omics studies often rely on pathway enrichment to interpret heterogeneous molecular changes, but pathway enrichment (PE)-based workflows inherit structural limitations of pathway resources, including curation lag, functional redundancy, and limited sensitivity to molecular states and interventions. Although recent work has explored using large language models (LLMs) to improve PE-based interpretation, the lack of a standardized benchmark for end-to-end multi-omics pathway mechanism elucidation has largely confined evaluation to small, manually curated datasets or ad hoc case studies, hindering reproducible progress. To address this issue, we introduce BIOME-Bench, constructed via a rigorous four-stage workflow, to evaluate two core capabilities of LLMs in multi-omics analysis: Biomolecular Interaction Inference and end-to-end Multi-Omics Pathway Mechanism Elucidation. We develop evaluation protocols for both tasks and conduct comprehensive experiments across multiple strong contemporary models. Experimental results demonstrate that existing models still exhibit substantial deficiencies in multi-omics analysis, struggling to reliably distinguish fine-grained biomolecular relation types and to generate faithful, robust pathway-level mechanistic explanations.
SLM-TTA: A Framework for Test-Time Adaptation of Generative Spoken Language Models
Venue: arXiv cs.SD 2025
Year: 2025

Spoken Language Models (SLMs) are increasingly central to modern speech-driven applications, but performance degrades under acoustic shift - real-world noise, reverberation, and microphone variation. Prior solutions rely on offline domain adaptation, which is post-hoc, data-intensive, and slow. We introduce the first test-time adaptation (TTA) framework for generative SLMs that process interleaved audio-text prompts. Our method updates a small, targeted subset of parameters during inference using only the incoming utterance, requiring no source data or labels. This stabilizes token distributions and improves robustness to acoustic variability without degrading core task accuracy. Evaluated on automatic speech recognition, speech translation, and 19 audio understanding tasks from AIR-Bench, our approach yields consistent gains under diverse corruptions. Because adaptation touches only a small fraction of weights, it is both compute- and memory-efficient, supporting deployment on resource-constrained platforms. This work enhances the robustness and adaptability of generative SLMs for real-world speech-driven applications.
Dream2Flow: Bridging Video Generation and Open-World Manipulation with 3D Object Flow
Venue: arXiv cs.RO 2025
Year: 2025

Generative video modeling has emerged as a compelling tool to zero-shot reason about plausible physical interactions for open-world manipulation. Yet, it remains a challenge to translate such human-led motions into the low-level actions demanded by robotic systems. We observe that given an initial image and task instruction, these models excel at synthesizing sensible object motions. Thus, we introduce Dream2Flow, a framework that bridges video generation and robotic control through 3D object flow as an intermediate representation. Our method reconstructs 3D object motions from generated videos and formulates manipulation as object trajectory tracking. By separating the state changes from the actuators that realize those changes, Dream2Flow overcomes the embodiment gap and enables zero-shot guidance from pre-trained video models to manipulate objects of diverse categories-including rigid, articulated, deformable, and granular. Through trajectory optimization or reinforcement learning, Dream2Flow converts reconstructed 3D object flow into executable low-level commands without task-specific demonstrations. Simulation and real-world experiments highlight 3D object flow as a general and scalable interface for adapting video generation models to open-world robotic manipulation. Videos and visualizations are available at https://dream2flow.github.io/.
GenZ: Foundational models as latent variable generators within traditional statistical models
Venue: arXiv cs.AI 2025
Year: 2025

We present GenZ, a hybrid model that bridges foundational models and statistical modeling through interpretable semantic features. While large language models possess broad domain knowledge, they often fail to capture dataset-specific patterns critical for prediction tasks. Our approach addresses this by discovering semantic feature descriptions through an iterative process that contrasts groups of items identified via statistical modeling errors, rather than relying solely on the foundational model's domain understanding. We formulate this as a generalized EM algorithm that jointly optimizes semantic feature descriptors and statistical model parameters. The method prompts a frozen foundational model to classify items based on discovered features, treating these judgments as noisy observations of latent binary features that predict real-valued targets through learned statistical relationships. We demonstrate the approach on two domains: house price prediction (hedonic regression) and cold-start collaborative filtering for movie recommendations. On house prices, our model achieves 12\% median relative error using discovered semantic features from multimodal listing data, substantially outperforming a GPT-5 baseline (38\% error) that relies on the LLM's general domain knowledge. For Netflix movie embeddings, our model predicts collaborative filtering representations with 0.59 cosine similarity purely from semantic descriptions -- matching the performance that would require approximately 4000 user ratings through traditional collaborative filtering. The discovered features reveal dataset-specific patterns (e.g., architectural details predicting local housing markets, franchise membership predicting user preferences) that diverge from the model's domain knowledge alone.
When Does the Silhouette Score Work? A Comprehensive Study in Network Clustering
Venue: arXiv cs.SI 2025
Year: 2025

Selecting the number of communities is a fundamental challenge in network clustering. The silhouette score offers an intuitive, model-free criterion that balances within-cluster cohesion and between-cluster separation. Albeit its widespread use in clustering analysis, its performance in network-based community detection remains insufficiently characterized. In this study, we comprehensively evaluate the performance of the silhouette score across unweighted, weighted, and fully connected networks, examining how network size, separation strength, and community size imbalance influence its performance. Simulation studies show that the silhouette score accurately identifies the true number of communities when clusters are well separated and balanced, but it tends to underestimate under strong imbalance or weak separation and to overestimate in sparse networks. Extending the evaluation to a real airline reachability network, we demonstrate that the silhouette-based clustering can recover geographically interpretable and market-oriented clusters. These findings provide empirical guidance for applying the silhouette score in network clustering and clarify the conditions under which its use is most reliable.
AODDiff: Probabilistic Reconstruction of Aerosol Optical Depth via Diffusion-based Bayesian Inference
Venue: arXiv cs.LG 2025
Year: 2025

High-quality reconstruction of Aerosol Optical Depth (AOD) fields is critical for Atmosphere monitoring, yet current models remain constrained by the scarcity of complete training data and a lack of uncertainty quantification.To address these limitations, we propose AODDiff, a probabilistic reconstruction framework based on diffusion-based Bayesian inference. By leveraging the learned spatiotemporal probability distribution of the AOD field as a generative prior, this framework can be flexibly adapted to various reconstruction tasks without requiring task-specific retraining. We first introduce a corruption-aware training strategy to learns a spatiotemporal AOD prior solely from naturally incomplete data. Subsequently, we employ a decoupled annealing posterior sampling strategy that enables the more effective and integration of heterogeneous observations as constraints to guide the generation process. We validate the proposed framework through extensive experiments on Reanalysis data. Results across downscaling and inpainting tasks confirm the efficacy and robustness of AODDiff, specifically demonstrating its advantage in maintaining high spatial spectral fidelity. Furthermore, as a generative model, AODDiff inherently enables uncertainty quantification via multiple sampling, offering critical confidence metrics for downstream applications.
PrivacyBench: A Conversational Benchmark for Evaluating Privacy in Personalized AI
Venue: arXiv cs.CL 2025
Year: 2025

Personalized AI agents rely on access to a user's digital footprint, which often includes sensitive data from private emails, chats and purchase histories. Yet this access creates a fundamental societal and privacy risk: systems lacking social-context awareness can unintentionally expose user secrets, threatening digital well-being. We introduce PrivacyBench, a benchmark with socially grounded datasets containing embedded secrets and a multi-turn conversational evaluation to measure secret preservation. Testing Retrieval-Augmented Generation (RAG) assistants reveals that they leak secrets in up to 26.56% of interactions. A privacy-aware prompt lowers leakage to 5.12%, yet this measure offers only partial mitigation. The retrieval mechanism continues to access sensitive data indiscriminately, which shifts the entire burden of privacy preservation onto the generator. This creates a single point of failure, rendering current architectures unsafe for wide-scale deployment. Our findings underscore the urgent need for structural, privacy-by-design safeguards to ensure an ethical and inclusive web for everyone.
SoK: Web3 RegTech for Cryptocurrency VASP AML/CFT Compliance
Venue: arXiv cs.CR 2025
Year: 2025

The decentralized architecture of Web3 technologies creates fundamental challenges for Anti-Money Laundering and Counter-Financing of Terrorism compliance. Traditional regulatory technology solutions designed for centralized financial systems prove inadequate for blockchain's transparent yet pseudonymous networks. This systematization examines how blockchain-native RegTech solutions leverage distributed ledger properties to enable novel compliance capabilities. We develop three taxonomies organizing the Web3 RegTech domain: a regulatory paradigm evolution framework across ten dimensions, a compliance protocol taxonomy encompassing five verification layers, and a RegTech lifecycle framework spanning preventive, real-time, and investigative phases. Through analysis of 41 operational commercial platforms and 28 academic prototypes selected from systematic literature review (2015-2025), we demonstrate that Web3 RegTech enables transaction graph analysis, real-time risk assessment, cross-chain analytics, and privacy-preserving verification approaches that are difficult to achieve or less commonly deployed in traditional centralized systems. Our analysis reveals critical gaps between academic innovation and industry deployment, alongside persistent challenges in cross-chain tracking, DeFi interaction analysis, privacy protocol monitoring, and scalability. We synthesize architectural best practices and identify research directions addressing these gaps while respecting Web3's core principles of decentralization, transparency, and user sovereignty.
Vibe Coding, Interface Flattening
Venue: arXiv cs.HC 2025
Year: 2025

Large language models are reshaping programming by enabling 'vibe coding': the development of softwares through natural-language interaction with model-driven toolchains. This article argues that vibe coding is best understood as interface flattening, a reconfiguration in which previously distinct modalities (GUI, CLI, and API) appear to converge into a single conversational surface, even as the underlying chain of translation from intention to machinic effect lengthens and thickens. Drawing on Friedrich Kittler's materialist media theory and Alexander Galloway's account of interfaces as sites of protocol control, the paper situates programming as a historically localised interface arrangement rather than an essential relation to computation. Through a materialist reconstruction of the contemporary vibe-coding stack, it shows how remote compute infrastructures, latency and connectivity, structured outputs, function/tool calling, and interoperability standards such as the Model Context Protocol relocate control and meaning-making power to model and protocol providers. The apparent democratisation of technical capability therefore depends on new dependencies and new literacies. By foregrounding the tension between experiential flattening and infrastructural thickening, I demonstrate how LLM-mediated development redistributes symbolic labour/power, obscures responsibility, and privatises competencies previously dispersed across programming communities, contributing a critical lens on the political economy of AI-mediated human-computer interaction.
ShowUI-$π$: Flow-based Generative Models as GUI Dexterous Hands
Venue: arXiv cs.CV 2025
Year: 2025

Building intelligent agents capable of dexterous manipulation is essential for achieving human-like automation in both robotics and digital environments. However, existing GUI agents rely on discrete click predictions (x,y), which prohibits free-form, closed-loop trajectories (e.g. dragging a progress bar) that require continuous, on-the-fly perception and adjustment. In this work, we develop ShowUI-$π$, the first flow-based generative model as GUI dexterous hand, featuring the following designs: (i) Unified Discrete-Continuous Actions, integrating discrete clicks and continuous drags within a shared model, enabling flexible adaptation across diverse interaction modes; (ii) Flow-based Action Generation for drag modeling, which predicts incremental cursor adjustments from continuous visual observations via a lightweight action expert, ensuring smooth and stable trajectories; (iii) Drag Training data and Benchmark, where we manually collect and synthesize 20K drag trajectories across five domains (e.g. PowerPoint, Adobe Premiere Pro), and introduce ScreenDrag, a benchmark with comprehensive online and offline evaluation protocols for assessing GUI agents' drag capabilities. Our experiments show that proprietary GUI agents still struggle on ScreenDrag (e.g. Operator scores 13.27, and the best Gemini-2.5-CUA reaches 22.18). In contrast, ShowUI-$π$ achieves 26.98 with only 450M parameters, underscoring both the difficulty of the task and the effectiveness of our approach. We hope this work advances GUI agents toward human-like dexterous control in digital world. The code is available at https://github.com/showlab/showui-pi.
PhysTalk: Language-driven Real-time Physics in 3D Gaussian Scenes
Venue: arXiv cs.GR 2025
Year: 2025

Realistic visual simulations are omnipresent, yet their creation requires computing time, rendering, and expert animation knowledge. Open-vocabulary visual effects generation from text inputs emerges as a promising solution that can unlock immense creative potential. However, current pipelines lack both physical realism and effective language interfaces, requiring slow offline optimization. In contrast, PhysTalk takes a 3D Gaussian Splatting (3DGS) scene as input and translates arbitrary user prompts into real time, physics based, interactive 4D animations. A large language model (LLM) generates executable code that directly modifies 3DGS parameters through lightweight proxies and particle dynamics. Notably, PhysTalk is the first framework to couple 3DGS directly with a physics simulator without relying on time consuming mesh extraction. While remaining open vocabulary, this design enables interactive 3D Gaussian animation via collision aware, physics based manipulation of arbitrary, multi material objects. Finally, PhysTalk is train-free and computationally lightweight: this makes 4D animation broadly accessible and shifts these workflows from a "render and wait" paradigm toward an interactive dialogue with a modern, physics-informed pipeline.
EF(X) Orientations: A Parameterized Complexity Perspective
Venue: arXiv cs.DS 2025
Year: 2025

The concept of fair orientations in graphs was introduced by Christodoulou, Fiat, Koutsoupias, and Sgouritsa in 2023, naturally modeling fair division scenarios in which resources are only contested by neighbors. In this model, vertices represent agents and undirected edges represent goods; edges have to be oriented towards one of their endpoints, i.e., allocated to one of their adjacent agents. Although EFX orientations (envy-free up to any good) have been extensively studied in this setting, EF orientations (envy-free) remain unexplored. In this work, we initiate their study, mostly under the lens of parameterized complexity, presenting various tractable cases, hardness results, and parameterizations. Our results concern both simple graphs and multigraphs. Interestingly, many of our results transfer to EFX orientations, thus complementing and improving upon previous work; notably, we answer an open question regarding the structural parameterized complexity of the latter problem on graphs of polynomially-bounded valuations. We also show that EF orientations are tractable in cases in which EFX orientations are not, particularly for binary valuations. Lastly, we consider charity in the orientation setting, establishing algorithms for finding the minimum amount of edges that have to be removed from a graph in order for EF(X) orientations to exist.
Thin Tree Verification is coNP-Complete
Venue: arXiv cs.CC 2025
Year: 2025

An $α$-thin tree $T$ of a graph $G$ is a spanning tree such that every cut of $G$ has at most an $α$ proportion of its edges in $T$. The Thin Tree Conjecture proposes that there exists a function $f$ such that for any $α> 0$, every $f(α)$-edge-connected graph has an $α$-thin tree. Aside from its independent interest, an algorithm which could efficiently construct an $O(1)/k$-thin tree for a given $k$-edge-connected graph would directly lead to an $O(1)$-approximation algorithm for the asymmetric travelling salesman problem (ATSP)(arXiv:0909.2849). However, it was not even known whether it is possible to efficiently verify that a given tree is $α$-thin. We prove that determining the thinness of a tree is coNP-hard.
AdaGReS:Adaptive Greedy Context Selection via Redundancy-Aware Scoring for Token-Budgeted RAG
Venue: arXiv cs.CL 2025
Year: 2025

Retrieval-augmented generation (RAG) is highly sensitive to the quality of selected context, yet standard top-k retrieval often returns redundant or near-duplicate chunks that waste token budget and degrade downstream generation. We present AdaGReS, a redundancy-aware context selection framework for token-budgeted RAG that optimizes a set-level objective combining query-chunk relevance and intra-set redundancy penalties. AdaGReS performs greedy selection under a token-budget constraint using marginal gains derived from the objective, and introduces a closed-form, instance-adaptive calibration of the relevance-redundancy trade-off parameter to eliminate manual tuning and adapt to candidate-pool statistics and budget limits. We further provide a theoretical analysis showing that the proposed objective exhibits epsilon-approximate submodularity under practical embedding similarity conditions, yielding near-optimality guarantees for greedy selection. Experiments on open-domain question answering (Natural Questions) and a high-redundancy biomedical (drug) corpus demonstrate consistent improvements in redundancy control and context quality, translating to better end-to-end answer quality and robustness across settings.
Reasoning in Action: MCTS-Driven Knowledge Retrieval for Large Language Models
Venue: arXiv cs.AI 2025
Year: 2025

Large language models (LLMs) typically enhance their performance through either the retrieval of semantically similar information or the improvement of their reasoning capabilities. However, a significant challenge remains in effectively integrating both retrieval and reasoning strategies to optimize LLM performance. In this paper, we introduce a reasoning-aware knowledge retrieval method that enriches LLMs with information aligned to the logical structure of conversations, moving beyond surface-level semantic similarity. We follow a coarse-to-fine approach for knowledge retrieval. First, we identify a contextually relevant sub-region of the knowledge base, ensuring that all sentences within it are relevant to the context topic. Next, we refine our search within this sub-region to extract knowledge that is specifically relevant to the reasoning process. Throughout both phases, we employ the Monte Carlo Tree Search-inspired search method to effectively navigate through knowledge sentences using common keywords. Experiments on two multi-turn dialogue datasets demonstrate that our knowledge retrieval approach not only aligns more closely with the underlying reasoning in human conversations but also significantly enhances the diversity of the retrieved knowledge, resulting in more informative and creative responses.
IMBWatch -- a Spatio-Temporal Graph Neural Network approach to detect Illicit Massage Business
Venue: arXiv cs.LG 2025
Year: 2025

Illicit Massage Businesses (IMBs) are a covert and persistent form of organized exploitation that operate under the facade of legitimate wellness services while facilitating human trafficking, sexual exploitation, and coerced labor. Detecting IMBs is difficult due to encoded digital advertisements, frequent changes in personnel and locations, and the reuse of shared infrastructure such as phone numbers and addresses. Traditional approaches, including community tips and regulatory inspections, are largely reactive and ineffective at revealing the broader operational networks traffickers rely on. To address these challenges, we introduce IMBWatch, a spatio-temporal graph neural network (ST-GNN) framework for large-scale IMB detection. IMBWatch constructs dynamic graphs from open-source intelligence, including scraped online advertisements, business license records, and crowdsourced reviews. Nodes represent heterogeneous entities such as businesses, aliases, phone numbers, and locations, while edges capture spatio-temporal and relational patterns, including co-location, repeated phone usage, and synchronized advertising. The framework combines graph convolutional operations with temporal attention mechanisms to model the evolution of IMB networks over time and space, capturing patterns such as intercity worker movement, burner phone rotation, and coordinated advertising surges. Experiments on real-world datasets from multiple U.S. cities show that IMBWatch outperforms baseline models, achieving higher accuracy and F1 scores. Beyond performance gains, IMBWatch offers improved interpretability, providing actionable insights to support proactive and targeted interventions. The framework is scalable, adaptable to other illicit domains, and released with anonymized data and open-source code to support reproducible research.